I came across a sample input file from Prof Kenneth Merz’s group and it is an equilibration input file. These are the contents:
I have 3 queries:
What is the utility of setting ntwv =1 ? ( have never tinkered with this parameter in AMBER ever)
Also the same query about ntave=10 (What is the importance of ntave parameter)
If we do not mention press0=1, will it not be the default value. I thought ntp =1 means we are setting the pressure at 1 atm.
Thanks
NPT MD w/No position restraints and PME (sander)
&cntrl
ntx = 5,
irest = 1,
ntpr = 1000,
ntwx = 1000,
ntwe = 1000,
ntwr = 1000,
ig = -1,
ntf = 1,
ntb = 2,
ntp = 1, pres0 = 1.0, taup = 2.0,gamma_ln = 2.0,
cut = 9.0,
iwrap = 1,
nsnb = 10,
nstlim = 1000000,
t = 0.0,
nscm = 1000,
dt = 0.001,
temp0 = 300.0,
tempi = 300.0,
ntt = 3,
tautp = 2.0,
ntc = 1,
iwrap=1, ioutfm=1, ntwv=-1,ntave=1000,
icfe = 1, ifsc = 1,
timask1=':1',
timask2=':2',
scmask1=':1.CB,HB1,HB2,HB3,',
scmask2=':2.CK1,CK2,NK1,CK3,NK2,CK4,HK1,HK2,HK3,',
clambda=0.5,
&end
&ewald
skinnb=2, nfft1=96, nfft2=96, nfft3=96,
/
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Received on Thu Apr 30 2020 - 12:30:01 PDT
